You are here

PyRosetta

Is a personal PC feasible to run PyRosetta?

Category: 
PyRosetta

Dear Sir or Madam,
Recently I encountered some problems (e.g. Runtime error, memory error) when running PyRosetta. I am not sure whether it is due to my old PC or my incorrect code. Can I ask do you think it is feasible to install

PyRosetta.Windows.64Bit.monolith.mode=release.branch=release-r10.exe

on a PC of

AMD Athlon(tm) II P360 Dual-Core Processor 2.30 GHz
4.00 GB
64-bit OS
Win 7 Ultimate, Service Pack 1
?

Or do you run your PyRosetta work on a cluster?

Post Situation: 

Calculating sasa per atom and atomid_map

Category: 
PyRosetta

Hi,

I am trying to calculate the sasa for each atom but I cannot get the arguments correct for rosetta.core.scoring.calc_per_atom_sasa.

I guess for "utility::vector1< Real > & rsd_sasa" I can use rosetta.utility.vector1_Real().

However, I have trouble with "id::AtomID_Map< Real > & atom_sasa". I tried rosetta.core.id.AtomID_Map_AtomID() but it doesn't match the C++ signature.

Post Situation: 

Bug in the BuildBindings.py with Linux kernel version

Category: 
Compilation
PyRosetta

Hi,
I think I have found a rather minor bug. It happens only with Linux. I don't know if there is a report system for this, so I am posting it on the forum.
Thanks for your work with Rosetta, it is really amazing.
Cyril

Context:
I am building pyrosetta from source, using the BuildPyRosetta.sh generated by rosetta/tools/PyRosetta.develop/DeployPyRosetta.py.

Post Situation: 

64 bit windows version of PyRosetta does not include rosetta.dll?

Category: 
PyRosetta

I was trying to download and use the 64 bit windows versions of PyRosetta, but when I tried to run "from rosetta import *" it can't find the rosetta.dll Any suggestions on how to get the 64 bit version of PyRosetta running on windows?

Post Situation: 

Argument error when running D120_Ligand_interface.py

Category: 
Docking
PyRosetta

Hi,

I am trying to run D120_Ligand_interface.py sample script with the provided test_lig.pdb and ATP.params. I have placed the ATP.params file into (in PyRosetta main directory) /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types and added the path of the ATP.params file to the file /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt. When I run the script (in ipython - run D120_Ligand_interface.py) I get the following error message.

Post Situation: 

Problems when inserting spin-label R1A

Category: 
Non-Canonical Peptides
PyRosetta

Dear all,

I would like to use the spin-lable R1A (implemented as part of Rosetta EPR).
In database/chemical/residue_type_sets/fa_standard/residue_types.txt I activated the needed lines

## Spin label types
# kills my unit tests???
residue_types/spin_labels/R1A.params

Although the “kills my unit tests???” comment is not very encouraging:=)

The problem is:

Post Situation: 

Capturing the output of scorefxn.show(pose)

Category: 
PyRosetta

I'm using PyRosetta-r21 on Ubuntu togather with IPython 2.0.0 notebooks. This works extremly well, with one small problem:
Some output is redirected to the console in which "ipython notebook" command was started instead of the notebook cell. 
So the question is: is it possible to capture the output of scorefxn.show(pose)?

I have tried to use the example in "test/T007_TracerIO.py"

 

Post Situation: 

Possible minor mistakes in SetPyRosettaEnvironment.sh (in r21 for Ubuntu)

Category: 
PyRosetta

Dear all,
There may be some minor mistakes in the SetPyRosettaEnvironment.sh in the r21 release of PyRosetta:

On line 34 "export LD_LIBRARY_PATH=$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
$PYROSETTA is not added to the LD_LIBRARY_PATH and "libboost_python.so.1.55.0.so" is consequently not found.
Corrected: "export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
(Or just move the offending so to rosseta subdir)

 

Post Situation: 

Approximating CHARMM energy by the rosetta scoring function

Category: 
Scoring
PyRosetta

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič

Post Situation: 

Pages

Subscribe to RSS - PyRosetta